Allied BBs shows the Massechusetts 16" hit on JB's (empty) secondary magazine , and it clearly shows the powder rooms above the shell rooms.
I checked, and yes, there are definitely separate shell and powder rooms. However, they are paired on the same levels. If you move forward from that G&D cross section, a shell room is directly forward of the labeled powder rooms, plus that one shell room beneath the powder. It appears that shell rooms are always forward of the powder. I don't know if the designers were thinking that actions would take place forward of the beam and were hoping to use the shells as splinter stoppers in that way...? I don't have a sufficiently detailed drawing of Gascogne to see how that arrangement would have differed. This is actually interesting. I'll ask around and see what I can come up with.
I would guess that the IJN would have followed RN WW1 practice and placed the shell rooms below the magazines.
I was thinking the same thing except I didn't know the RN was arranging things with the powder on top. But Kongo and Fuso also had the shell rooms above the powder. I agree this is a better arrangement for the protection afforded by the shell bodies, even in the days of more volatile bursters.